20-52086094-C-T

Variant names:

• chr20-52086094-C-T
• rs6013382
• ENST00000361387.6:c.1229-828G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_199427.3(ZFP64):​c.1229-828G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.48 in 152,030 control chromosomes in the GnomAD database, including 17,846 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.48 (17846 hom., cov: 33)
• Consequence: ZFP64 NM_199427.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.219
• Publications: 12 publications found

Genes affected

ZFP64 (HGNC:15940): (ZFP64 zinc finger protein) Predicted to enable DNA binding activity and metal ion binding activity. Predicted to be involved in positive regulation of cytokine production and positive regulation of transcription by RNA polymerase II. Predicted to act upstream of or within positive regulation of mRNA splicing, via spliceosome. Predicted to be active in nucleus. [provided by Alliance of Genome Resources, Apr 2022]

ENSG00000287511 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.529 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_199427.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZFP64	NM_199427.3		c.1229-828G>A		intron	N/A	NP_955459.2	Q9NTW7-1
	ZFP64	NM_001319146.2		c.572-828G>A		intron	N/A	NP_001306075.1	Q9NTW7-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZFP64	ENST00000361387.6	TSL:1	c.1229-828G>A		intron	N/A	ENSP00000355179.2	Q9NTW7-1
	ZFP64	ENST00000371518.6	TSL:1	c.1228+2298G>A		intron	N/A	ENSP00000360573.2	Q9NTW7-3
	ZFP64	ENST00000371523.8	TSL:2	c.572-828G>A		intron	N/A	ENSP00000360578.4	Q9NTW7-2

Frequencies

GnomAD3 genomes AF: 0.480 AC: 72957 AN: 151912 Hom.: 17828 Cov.: 33

Gnomad AFR AF: 0.535

Gnomad AMI AF: 0.568

Gnomad AMR AF: 0.417

Gnomad ASJ AF: 0.379

Gnomad EAS AF: 0.331

Gnomad SAS AF: 0.402

Gnomad FIN AF: 0.538

Gnomad MID AF: 0.297

Gnomad NFE AF: 0.476

Gnomad OTH AF: 0.422

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.480 AC: 73020 AN: 152030 Hom.: 17846 Cov.: 33 AF XY: 0.479 AC XY: 35562 AN XY: 74308

African (AFR) AF: 0.535 AC: 22194 AN: 41474

American (AMR) AF: 0.417 AC: 6368 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.379 AC: 1314 AN: 3468

East Asian (EAS) AF: 0.331 AC: 1714 AN: 5176

South Asian (SAS) AF: 0.402 AC: 1936 AN: 4816

European-Finnish (FIN) AF: 0.538 AC: 5671 AN: 10538

Middle Eastern (MID) AF: 0.296 AC: 87 AN: 294

European-Non Finnish (NFE) AF: 0.476 AC: 32322 AN: 67970

Other (OTH) AF: 0.423 AC: 896 AN: 2116

Alfa AF: 0.467 Hom.: 72287

Bravo AF: 0.471

Asia WGS AF: 0.361 AC: 1256 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	6.6
DANN	Benign	0.66
PhyloP100		-0.22
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.050		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs6013382; hg19: chr20-50702633;